Who am I?

• Education
  • B.Sc. Bioarchaeology (University of York, UK)
  • M.Sc. Naturwissenschaftliches Archäologie (University of Tübingen, DE)
  • Ph.D. Archaeogenetics (MPI-SHH / MPI-EVA, DE)
• Experience
  • Number of genetics classes taken: 0
  • Number of bioinformatics classes taken: 0

Today we will

1. Introduce what DNA sequencing is
2. Explain how Illumina NGS sequencing data is generated
3. How to evaluating NGS data [Practical]

What is DNA?

Deoxyribonucleic acid (/diːˈɒksɪˌraɪboʊnjuːˌkliːɪk, -ˌkleɪ-/ (DNA) is a molecule composed of two polynucleotide chains that coil around each other to form a double helix carrying genetic instructions for the development, functioning, growth and reproduction of all known organisms and many viruses. - Wikipedia

What is DNA?

By Zephyris (CC-BY-3.0 SA)

What is DNA?

By Pradana Aumars (CC-BY-4.0 SA)

The rules

• Four nucleotides
  • Pyrimidines: Cytosine, Thymine
  • Purines: Guanine Adenine &
• Base pairing: one pyrimidine with one purine
  • C with G (think: CGI)
  • A to T (think: AT-AT walker)
• Complementary
  • C on one strand, G on the other (or v.v.)
  • A on one strand, T on the other (or v.v.)

The rules

• Make copy of a DNA strand with a polymerase
  • Unwind the DNA
  • Separate the strands
  • Make new strand: find a C, get new G (etc)

By Madprime (CC-BY-3.0 SA)

How do we get DNA?

By CFCF (CC-BY-4.0 SA)

What is Sequencing?

Converting the chemical nucleotides of a DNA molecule

to

ACTG on your computer screen

What is NGS?

NGS: Next Generation Sequencing

• MASSIVELY multiplexed!
• Sequence millions and millions and millions and millions of DNA reads at once!

Not really ‘next’ anymore, consider it more ‘second’ generation (see: Nanopore)

Market leader:

How does it work?

cat 1.fastq 2.fastq